Cell-type specific aptamer-siRNA delivery system for HIV-1 therapy

ABSTRACT

The present invention relates to compositions and methods for delivery of siRNA to specific cells or tissue. More particularly, the present invention relates to compositions and methods for cell type-specific delivery of anti-HIV siRNAs via fusion to an anti-gp120 aptamer.

CROSS-REFERENCE TO RELATED APPLICATION

The present application is a continuation of U.S. patent applicationSer. No. 13/230,088, filed 12 Sep. 2011, which is a continuation of U.S.patent application Ser. No. 12/328,994, filed 5 Dec. 2008, now U.S. Pat.No. 8,030,290, which in turn claims benefit under 35 U.S.C. §119(e) ofU.S. Provisional Patent Application No. 60/996,850, filed 7 Dec. 2007.Each application is incorporated herein by reference in its entirety.

STATEMENT OF FEDERALLY SPONSORED RESEARCH

The present invention was made in part with Government support underGrant Numbers AI29329 awarded by the National Institutes of Health,Bethesda, Md. The Government has certain rights in this invention.

BACKGROUND OF THE INVENTION

The present invention relates to compositions and methods for deliveryof siRNA to specific cells or tissue. More particularly, the presentinvention relates to compositions and methods for cell type-specificdelivery of anti-HIV siRNAs via fusion to an anti-gp120 aptamer.

The publications and other materials used herein to illuminate thebackground of the invention, and in particular, cases to provideadditional details respecting the practice, are incorporated byreference, and for convenience are referenced in the following text byauthor and date and are listed alphabetically by author in the appendedbibliography.

RNA interference (RNAi) is a process of sequence-specificpost-transcriptional gene silencing triggered by small interfering RNAs(siRNA). The silencing is sequence specific and one of the two strandsof the siRNA guides the RNA induced silencing complex (RISC) to thecomplementary target, resulting in cleavage and subsequent destructionof the target RNA (1). RNAi is rapidly becoming one of the methods ofchoice for gene function studies, and is also being exploited fortherapeutic applications (2, 3). The successful therapeutic applicationsof RNAi are critically dependent upon efficient intracellular deliveryof siRNAs (3).

Currently, there are several methods to deliver siRNA in vivo. These canbe divided into physical and mechanical methods (hydrodynamic tail veininjections in mice (4-6), electroporation (7-9), ultrasound (10), andthe gene gun (11)); local administration (3) (intravenous injection(12), intraperitoneal injection, subcutaneous injection); and chemicalmethods (cationic lipids (13, 14), polymers (15-20), and peptides(21-24)). However, the delivery efficiency (desired dose),uncontrollable biodistribution and delivery-related toxicitities must becarefully analyzed.

Recently, the cell type-specific delivery of siRNAs has been achievedusing aptamer-siRNA chimeras (25). In this system, the aptamer portionmediated binding to the prostate-specific membrane antigen (PSAM), acell-surface receptor and the siRNAs linked to the aptamer wasselectively delivered into PSMA expressing cells resulting in silencingof target transcripts both in cell culture and in vivo followingintratumoral delivery. In a similar study (26) a modular streptavidinbridge was used to connect lamin A/C or GAPDH siRNAs to the PSMAaptamer. Consequently, this system induced silencing of the targetedgenes only in cells expressing the PSMA receptor.

Thus, it is desired to develop compositions and methods for cell- ortissue-specific delivery of siRNA molecules for treatment.

SUMMARY OF THE INVENTION

The present invention relates to compositions and methods for deliveryof siRNA to specific cells or tissue. More particularly, the presentinvention relates to compositions and methods for cell type-specificdelivery of anti-HIV siRNAs via fusion to an anti-gp120 aptamer.

In one aspect, the present invention provides a molecule for deliveringsiRNA to cells or tissues. In one embodiment, the molecule comprises thefusion of an aptamer that is specific for a cell or tissue with a siRNAto be delivered to the cell or tissue. In another embodiment, theaptamer is an anti-gp120 aptamer and the siRNA is directed againstHIV-1. In a further embodiment, the siRNA is an anti-tat/rev siRNA. Inone embodiment, the aptamer-sense strand siRNA is encoded by a DNAtemplate. In another embodiment, the DNA template is transcribed toproduce the aptamer-sense strand siRNA molecule. In a furtherembodiment, the aptamer-sense strand siRNA is annealed with an antisensestrand siRNA to produce the aptamer-siRNA molecule. In one embodiment,pharmaceutical compositions comprising the aptamer-siRNA molecule areprovided.

In a second aspect, the present invention provides a method for deliveryof siRNA to specific cells or tissue. In one embodiment, the methodcomprises administering a pharmaceutical composition comprising amolecule for delivering siRNA to cells or tissues. In one embodiment,the molecule comprises the fusion of an aptamer that is specific for acell or tissue with a siRNA to be delivered to the cell or tissue. Inanother embodiment, the aptamer is an anti-gp120 aptamer and the siRNAis directed against HIV-1. In a further embodiment, the siRNA is ananti-tat/rev siRNA. In another embodiment, the anti-gp120 aptamer-siRNAis delivered to HIV infected cells.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 shows the predicted secondary structure for anti-gp120aptamer-siRNA chimeras. The sequence of the aptamer/linker/sense strandis SEQ ID NO:1, and the sequence of the antisense strand is SEQ ID NO:2.The region of anti-gp120 aptamer responsible for binding to gp120 isoutlined in green. The siRNA part of the chimera consists of 27 bps asan example here, targeting Site-I of HIV-1 tat/rev. Two mutated chimerasM-1 (mutant aptamer) and M-2 (mutant siRNA) were constructed asexperimental controls. Mutated regions are shown in magenta.

FIG. 2A shows a binding affinity assay. Cy3-labeled RNAs were tested forbinding to CHO-gp160 cells and CHO-EE control cells. Cell surfacebinding of Cy3-labeled aptamer-siRNA chimeras were assessed by flowcytometry.

FIG. 2B shows the binding and uptake of Ch 1 to CHO-gp160 cells.CHO-gp160 cells and CHO-EE control cells were grown on chamber slidesand incubated with 20 nM of Ch 1 in culture medium for 2 hours. Cellswere washed in PBS three times, fixed and stained with DIO (a plasmamembrane dye), washed and analyzed by confocal microscopy.

FIGS. 3A and 3B show the analysis of chimera processing. 21-23 nt RNAfragments are produced following incubation of chimera RNAs in HCT116cell extracts. FIG. 3A: Chimera sense strands (SEQ ID NO:1) wereannealed with equal molar equivalents of 5′-end P³²-labeled antisenseoligos (SEQ ID NO:2). The FIG. 3B: The cleavage products or denaturedstrands were visualized following denaturing polyacrylamide-gelelectrophoresis. Note that the major Dicer product (marked by a whitearrow) of the 27 mer aptamers is processed from the 5′ end of theantisense strand since the 21 base product harbors the 5′ ³²P label.

FIG. 4A shows that aptamer-siRNA chimeras-mediate silencing of pNL4-3luciferase. CHO-gp160 cells or CHO-EE cells transfected with pNL4-3 lucwere incubated with 200 nM of the experimental RNAs in the presence orabsence of the transfection reagent lipofectamine 2000. In the absenceof the transfection reagent inhibition of pNL4-3 luc expression was onlyobserved for CHO-gp160 cells. These results are consistent with theaptamer mediated binding to gp160 and internalization of the chimerafollowed by processing into siRNAs. The data were normalized withRenilla luciferase expression and represent the average of threereplicate assays.

FIG. 4B shows that cleaved mRNA from CHO-gp160 cells previouslytransfected with either saline (untreated), Tat-Rev site I 27-mer siRNA,21-mer siRNA, Ch L-1 and Ch L-2 RNAs, was ligated to an RNA adaptor andreverse transcribed using a gene-specific primer. Depicted is an agarosegel electorphoresis of the 5′-RACE-PCR amplification products using aprimer specific to the RNA adaptor and a reverse primer (GSP-Rev-2) toRev-EGFP, indicated specific siRNA-mediated cleavage products ofRev-EGFP mRNA. The sequence of the “21+2 mer antisense strand” is SEQ IDNO:3. The sequence of the “Target sequence of Tat/Rev” is SEQ ID NO:4.The sequence of the “27+2 mer antisense strand” is SEQ ID NO:2.

FIG. 5A show Northern blots of infected CEM cells. Infected CEM cellswere directly treated with siRNA and Chimeras. The 27 Chimera RNA ispartially processed to a 21 mer siRNA following uptake into the CEMcells. Total RNAs were hybridized with a 21-mer P³²-labeledoligonucleotide probe. U6 RNA was used as an internal loading control.

FIG. 5B shows aptamer-mediated inhibition of expression of tat/rev ininfected CEM cells. Cells were incubated with the wild type aptamer orCh L-1 for 7 days prior to RNA extraction. Gene expression for Tat/revand GAPDH was assayed by qRT-PCR. Data represent the average of threereplicates.

FIG. 5C shows that chimera RNAs inhibit HIV infection. HIV-1 NL4-3 wasincubated with the various RNAs at 37° C. for 1 h. Subsequently, thetreated virions were used to infect CEM cells. The culture supernatantwas collected at different time (7 d, 11 d, 15 d and 18 d) for p24antigen analyses. Data represent the average of duplicate assays.

FIG. 5D shows that the siRNAs delivered by the chimera RNAs inhibitHIV-1 replication in previously infected CEM cells. 1.5×10⁴ infected CEMcells and 3.5×10⁴ uninfected CEM cells were incubated at 37 C with thevarious RNAs at a final concentration of 400 nM. The culture supernatantwas collected at different time points (3 d, 5 d, 7 d and 9 d) for p24antigen analyses. Data represent the average of triplicate measurementsof p24.

FIGS. 6A and 6B show IFN assays. IFN-β, the interferon response geneencoding P56 (CDKL2) and OAS1, mRNAs were measured by quantitativeRT-PCR. The expression of these interferon response genes was, notsignificantly induced by the siRNAs or chimeric RNAs, whereas expressionof these genes was induced by poly(IC) in HEK 293 cells (FIG. 6A) or byIFN-alpha in infected CEM cells (FIG. 6B). Gene expression levels arenormalized to GAPDH mRNA expression levels. The data represent theaverage of triplicate measurements.

FIG. 7 shows the gene silencing activity and strand selectivity ofchimeras RNAs and siRNA. Dual luciferase assays of psiCHECK sense andanti-sense targets are shown. All RNAs are normalized to the valued ofthe corresponding buffer control. The strand selectivity was calculatedas: R_(buffer)=1.0; R_(27mer siRNA)=2.2; R_(21mer siRNA)=4.9;R_(Ch L-1)=3.2; R_(Ch L-2)=1.9; R_(Ch 1)=2.9; R_(Ch 2)=1.6; R_(M-2)=1.2,respectively.

FIG. 8 shows that images were combined and deconvoluted to reconstruct athree-dimensional image. Three-dimensional image reconstruction showslocalization of the Cy3-labeled Ch 1 in a single cell.

FIGS. 9A-9C show the RACE PCR sequences. FIG. 9A: For the 27 mer duplexRNA, the RACE PCR product was cloned into TA vector and sequenced. Theresulting sequence is identified as “RACE PCR Product exact sequence(243 bp)” and is SEQ ID NO:5. FIG. 9B: For the 21 mer duplex RNA, theRACE PCR product was gel purified and directly sequenced using relativeforward primer (5′-cDNA primer 1) and reverse primer (GSP primer 2). Theresulting sequence is identified as “RACE PCR Product exact sequence(249 bp)” and is SEQ ID NO:6. FIG. 9C: The positions of the varioussequences within the HIV-1 nucleic acid sequence (SEQ ID NO:7) is shown.

FIGS. 10A and 10B show an immunofluorescence assay of HIV-1 p17. HIV-1infected CEM cells were incubated with 400 no aptamer or chimeras (ChL-1 and Ch L-2) in culture medium for 24 hours (FIG. 10A) and 72 hours(FIG. 10B). Cells were washed with PBs, fixed, permeabilized and blockedwith NGtS. After incubation with primary antibody (anti-p17),FITC-conjugated secondary antibody (Ho-α-Mu-FITC) was added to staincells. Cells were washed, resuspended in 15 μL hard mounting medium andspotted on a microscopy slide for confocal microscopy.

FIGS. 11A-11C show the secondary structure and binding activity assay ofselected aptamers against HIV-1_(Bal) gp120. FIG. 11A: The predicatedsecondary structures of anti-gp120 aptamer A-1 (SEQ ID NO:8) and B-68(SEQ ID NO:9). FIG. 11B: Gel shift assay. The 5′-end P³² labeledindividual aptamer was incubated with the increasing gp120 protein. Thebinding reaction mixtures were preformed gel shift assay. FIG. 11C: Thefirst K_(d) of the binding interaction was calculated from the gel shiftassay.

FIGS. 12A and 12B show binding and uptake of aptamer A-1 to CHO-gp160cells. FIG. 12A: Binding affinity assay. Cy3-labeled RNAs were testedfor binding to CHO-gp160 cells and CHO-EE control cells. Cell surfacebindings of Cy3-labeled RNAs were assessed by flow cytometry. Aptamer 1was one of reported gp120 aptamers. The 2^(nd) RNA pool was anon-relevant RNA control. FIG. 12B: CHO-gp160 cells and CHO-EE controlcells were grown on chamber slides and incubated with 40 nM of A-1 inculture medium for 2 hours. Cells were washed in PBS three times, fixedand stained with DIO (a plasma membrane dye), washed and analyzed byconfocal microscopy.

FIG. 13 shows that the selected anti-gp120 aptamers inhibited HIV-1replication in previously infected CEM cells. 1.5×10⁴ infected CEM cellsand 3.5×104 uninfected CEM cells were incubated at 37° C. with thevarious RNAs at a final concentration of 400 nM. The culture supernatantwas collected at different time points (3 d, 5 d, 7 d, 9 d and 11 d) forp24 antigen analyses. Data represent the average of triplicatemeasurements of p24.

FIGS. 14A and 14B show the aptamer-based approach for siRNA delivery.FIG. 14A: The design of aptamer-siRNA chimeric RNAs. The region ofanti-gp120 aptamer responsible for binding to gp120 (the A-1 aptamer orthe B-68 aptamer) and the siRNA part of the chimera consists of 27 bpsas an example here, targeting Site-I of HIV-1 tat/rev. FIG. 14B: Theaptamer-siRNA chimeric RNAs that have comparable K_(d) valuesspecifically bind with HIV_(Bal) gp120 protein as shown in this gelshift assay.

FIGS. 15A-15D show dual inhibition on HIV-1 infection mediated byaptamer-siRNA chimeras. Both anti-gp120 aptamer and aptamer-siRNAchimeras neutralized the HIV-1 infection in CEM cells (FIG. 15A) andPBMC culture (FIG. 15C), respectively. The chimeras (Ch A-1/Ch B-68)showed better inhibition than aptamer alone. The siRNA delivered byaptamers down-regulated target gene expression in CEM (FIG. 15B) andPBMC (FIG. 15D) as measured by Tat/Rev expression (qRT-PCR).

DETAILED DESCRIPTION OF THE INVENTION

The present invention relates to compositions and methods for deliveryof siRNA to specific cells or tissue. More particularly, the presentinvention relates to compositions and methods for cell type-specificdelivery of anti-HIV siRNAs via fusion to an anti-gp120 aptamer.

In accordance with the present invention, we demonstrate celltype-specific delivery of anti-HIV siRNAs via fusion to an anti-gp120aptamer. The envelope glycoprotein is expressed on the surface of HIV-1infected cells, allowing binding and internalization of theaptamer-siRNA chimeric molecules. We demonstrate that the anti-gp120aptamer-siRNA chimera is specifically taken up by cells expressing HIV-1gp120, and the appended siRNA is processed by Dicer, releasing ananti-tat/rev siRNA which in turn inhibits HIV replication. We show forthe first time a dual functioning aptamer-siRNA chimera in which boththe aptamer and the siRNA portions have potent anti-HIV activities andthat gp120 expressed on the surface of HIV infected cells can be usedfor aptamer mediated delivery of anti-HIV siRNAs.

In one aspect, the present invention provides a molecule for deliveringsiRNA to cells or tissues. In one embodiment, the molecule comprises thefusion of an aptamer that is specific for a cell or tissue with a siRNAto be delivered to the cell or tissue. In another embodiment, theaptamer is an anti-gp120 aptamer and the siRNA is directed againstHIV-1. In a further embodiment, the siRNA is an anti-tat/rev siRNA. Inone embodiment, the aptamer-sense strand siRNA is encoded by a DNAtemplate. In another embodiment, the DNA template is transcribed toproduce the aptamer-sense strand siRNA molecule. In a furtherembodiment, the aptamer-sense strand siRNA is annealed with an antisensestrand siRNA to produce the aptamer-siRNA molecule. In one embodiment,pharmaceutical compositions comprising the aptamer-siRNA molecule areprovided.

Thus, in accordance with the present invention, advantage of the gp120glycoprotein (27, 28) binding properties of an anti-gp120 RNA aptamerwas taken in order to explore the potential of using this aptamer fordelivery of anti-HIV siRNAs into HIV infected cells. Based upon previousstudies (29, 30), the aptamer as a chimeric transcript with a Dicersubstrate RNA duplex (25-30 nt) was tested.

An “aptamer” refers to a nucleic acid molecule that is capable ofbinding to a particular molecule of interest with high affinity andspecificity (41-42). The binding of a ligand to an aptamer, which istypically RNA, changes the conformation of the aptamer and the nucleicacid within which the aptamer is located. The conformation changeinhibits translation of an mRNA in which the aptamer is located, forexample, or otherwise interferes with the normal activity of the nucleicacid. Aptamers may also be composed of DNA or may comprise non-naturalnucleotides and nucleotide analogs. An aptamer will most typically havebeen obtained by in vitro selection for binding of a target molecule.However, in vivo selection of an aptamer is also possible. An aptamerwill typically be between about 10 and about 300 nucleotides in length.More commonly, an aptamer will be between about 30 and about 100nucleotides in length. See, e.g., U.S. Pat. No. 6,949,379, incorporatedherein by reference.

A Dicer substrate RNA duplex is a dsRNA that has been designed to bepreferentially processed by the Dicer complex rather than feedingdirectly into the RISC complex. Such dsRNAs have been found to haveenhanced potency/efficacy and duration of effect, as compared tocorresponding siRNA agents. See, U.S. Patent Application PublicationNos. 2005/0244858, 2005/0277610 and 2007/0265220, each incorporatedherein by reference, for descriptions of Dicer substrate RNA duplexes.

In accordance with the present invention, an anti-gp120 aptamer-siRNAchimera is prepared in which one strand of a 27 mer siRNA is covalentlyattached to the aptamer, and the second strand is base paired to thefirst strand. Similarly an anti-gp120 aptamer-siRNA chimera is preparedin which one strand of a 21 mer siRNA is covalently attached to theaptamer, and the second strand is base paired to the first strand. Thesechimeras were used to compare the use of a siRNA based on a 27 base pairdsRNA with the use of an siRNA based on a 21 base pair dsRNA. Theanti-gp120 aptamer binding to the R5 version of HIV-1 gp120 has beenpreviously demonstrated (31). This aptamer was shown to neutralize HIV-1infectivity (31-33) by direct binding to gp120 in virions. It wasdesired to determine whether or not the anti-gp120 aptamer could provideselective binding and subsequent internalization into HIV infected cellswhich should express gp120 on the cell surface. Although the aptameralone provided some inhibitory function when tested in this setting, thesiRNA chimeras provided more potent inhibition than the aptamer alone,suggesting cooperativity between the siRNA and aptamer portions ininhibiting HIV replication and spread. The results described hereindemonstrate that the gp120 aptamer-siRNA chimeras are internalized incells expressing gp120 either ectopically or from HIV infection, andmoreover the chimeric RNAs provide potent and lasting inhibition of HIVreplication in T-cells in culture. These results support the concept ofusing aptamer-siRNA conjugates for systemic treatment of HIV infection.This approach has the major advantage of not relying upon gene therapy,and the siRNAs can be changed or multiplexed to avert viral resistance.

The aptamer-siRNA can also be designed to be more efficiently processedby Dicer. According to this embodiment, the dsRNA has a lengthsufficient such that it is processed by Dicer to produce anaptamer-siRNA and at least one of the following properties: (i) thedsRNA is asymmetric, e.g., has a 3′ overhang on the sense strand and(ii) the dsRNA has a modified 3′ end on the antisense strand to directorientation of Dicer binding and processing of the dsRNA to an activesiRNA. According to this embodiment, the longest strand in the dsRNAcomprises 24-30 nucleotides. In one embodiment, the sense strandcomprises 24-30 nucleotides and the antisense strand comprises 22-28nucleotides. Thus, the resulting dsRNA has an overhang on the 3′ end ofthe sense strand. The overhang is 1-3 nucleotides, such as 2nucleotides. The antisense strand may also have a 5′ phosphate. See,e.g., U.S. Patent Application Publication Nos. 2005/0244858,2005/0277610 and 2007/0265220 for the design of dsRNA molecules that aremore efficiently processed by Dicer.

In addition to the modifications discussed above, additionalmodifications can be made to the aptamer-siRNA molecule. Modificationscan be included in the dsRNA, i.e., the aptamer-siRNA molecule, so longas the modification does not prevent the dsRNA composition from servingas a substrate for Dicer. In one embodiment, one or more modificationsare made that enhance Dicer processing of the dsRNA. In a secondembodiment, one or more modifications are made that result in moreeffective RNAi generation. In a third embodiment, one or moremodifications are made that support a greater RNAi effect. In a fourthembodiment, one or more modifications are made that result in greaterpotency per each dsRNA molecule to be delivered to the cell.Modifications can be incorporated in the 3′-terminal region, the5′-terminal region, in both the 3′-terminal and 5′-terminal region or insome instances in various positions within the sequence. With therestrictions noted above in mind any number and combination ofmodifications can be incorporated into the dsRNA. Where multiplemodifications are present, they may be the same or different.Modifications to bases, sugar moieties, the phosphate backbone, andtheir combinations are contemplated. Either 5′-terminus can bephosphorylated.

In another embodiment, the antisense strand is modified for Dicerprocessing by suitable modifiers located at the 3′ end of the antisensestrand, i.e., the dsRNA is designed to direct orientation of Dicerbinding and processing. Suitable modifiers include nucleotides such asdeoxyribonucleotides, dideoxyribonucleotides, acyclonucleotides and thelike and sterically hindered molecules, such as fluorescent moleculesand the like. Acyclonucleotides substitute a 2-hydroxyethoxymethyl groupfor the 2′-deoxyribofuranosyl sugar normally present in dNMPs. Othernucleotide modifiers could include 3′-deoxyadenosine (cordycepin),3′-azido-3′-deoxythymidine (AZT), 2′,3′-dideoxyinosine (ddI),2′,3′-dideoxy-3′-thiacytidine (3TC),2′,3′-didehydro-2′,3′-dideoxythymidine (d4T) and the monophosphatenucleotides of 3′-azido-3′-deoxythymidine (AZT),2′,3′-dideoxy-3′-thiacytidine (3TC) and2′,3′-didehydro-2′,3′-dideoxythymidine (d4T). In one embodiment,deoxynucleotides are used as the modifiers. When nucleotide modifiersare utilized, 1-3 nucleotide modifiers, or 2 nucleotide modifiers aresubstituted for the ribonucleotides on the 3′ end of the antisensestrand. When sterically hindered molecules are utilized, they areattached to the ribonucleotide at the 3′ end of the antisense strand.Thus, the length of the strand does not change with the incorporation ofthe modifiers. In another embodiment, the invention contemplatessubstituting two DNA bases in the dsRNA to direct the orientation ofDicer processing. In a further invention, two terminal DNA bases arelocated on the 3′ end of the antisense strand in place of tworibonucleotides forming a blunt end of the duplex on the 5′ end of thesense strand and the 3′ end of the antisense strand, and atwo-nucleotide RNA overhang is located on the 3′-end of the sensestrand. This is an asymmetric composition with DNA on the blunt end andRNA bases on the overhanging end.

Examples of modifications contemplated for the phosphate backboneinclude phosphonates, including methylphosphonate, phosphorothioate, andphosphotriester modifications such as alkylphosphotriesters, and thelike. Examples of modifications contemplated for the sugar moietyinclude 2′-alkyl pyrimidine, such as 2′-O-methyl, 2′-fluoro, amino, anddeoxy modifications and the like (see, e.g., Amarzguioui et al. (51)).Examples of modifications contemplated for the base groups includeabasic sugars, 2-O-alkyl modified pyrimidines, 4-thiouracil,5-bromouracil, 5-iodouracil, and 5-(3-aminoallyl)-uracil and the like.Locked nucleic acids, or LNA's, could also be incorporated. Many othermodifications are known and can be used so long as the above criteriaare satisfied. Examples of modifications are also disclosed in U.S. Pat.Nos. 5,684,143, 5,858,988 and 6,291,438 and in U.S. published patentapplication No. 2004/0203145 A1, each incorporated herein by reference.Other modifications are disclosed in Herdewijn (52), Eckstein (53),Rusckowski et al. (54), Stein et al. (55) and Vorobjev et al. (56), eachincorporated herein by reference.

Additionally, the aptamer-siRNA structure can be optimized to ensurethat the oligonucleotide segment generated from Dicer's cleavage will bethe portion of the oligonucleotide that is most effective in inhibitinggene expression. For example, in one embodiment of the invention a 27-bpoligonucleotide of the dsRNA structure is synthesized wherein theanticipated 21 to 22-bp segment that will inhibit gene expression islocated on the 3′-end of the antisense strand. The remaining baseslocated on the 5′-end of the antisense strand will be cleaved by Dicerand will be discarded. This cleaved portion can be homologous (i.e.,based on the sequence of the target sequence) or non-homologous andadded to extend the nucleic acid strand.

In addition, the aptamer and the aptamer-siRNA chimera can be modifiedso that they contain 2′F-CTP and 2′F-UTP nucleotides to produce RNA thatis resistant to RNase A degradation. Such modified RNA molecules aremade using conventional techniques well known to the skilled artisan.

RNA may be produced enzymatically or by partial/total organic synthesis,and modified ribonucleotides can be introduced by in vitro enzymatic ororganic synthesis. In one embodiment, each strand is preparedchemically. Methods of synthesizing RNA molecules are known in the art.

In a second aspect, the present invention provides a method for deliveryof siRNA to specific cells or tissue. In one embodiment, the methodcomprises administering a pharmaceutical composition comprising amolecule for delivering siRNA to cells or tissues. In one embodiment,the molecule comprises the fusion of an aptamer that is specific for acell or tissue with a siRNA to be delivered to the cell or tissue. Inanother embodiment, the aptamer is an anti-gp120 aptamer and the siRNAis directed against HIV-1. In a further embodiment, the siRNA is ananti-tat/rev siRNA. In another embodiment, the anti-gp120 aptamer-siRNAis delivered to HIV infected cells.

The aptamer-siRNA molecule can be suitably formulated and introducedinto the environment of the cell by any means that allows for asufficient portion of the sample to enter the cell to induce genesilencing, if it is to occur. Many formulations for dsRNA are known inthe art and can be used. See, e.g., U.S. published patent applicationNos. 2004/0203145 A1 and 2005/0054598 A1, each incorporated herein byreference. For example, siRNA can be formulated in buffer solutions suchas phosphate buffered saline solutions, liposomes, micellar structures,and capsids. Formulations of siRNA with cationic lipids can be used tofacilitate transfection of the dsRNA into cells. For example, cationiclipids, such as lipofectin (U.S. Pat. No. 5,705,188, incorporated hereinby reference), cationic glycerol derivatives, and polycationicmolecules, such as polylysine (published PCT International ApplicationWO 97/30731, incorporated herein by reference), can be used. Suitablelipids include Oligofectamine, Lipofectamine (Life Technologies), NC388(Ribozyme Pharmaceuticals, Inc., Boulder, Colo.), or FuGene 6 (Roche)all of which can be used according to the manufacturer's instructions.

It can be appreciated that the method of introducing an aptamer-siRNAmolecule into the environment of the cell will depend on the type ofcell and the make up of its environment. For example, when the cells arefound within a liquid, one preferable formulation is with a lipidformulation such as in lipofectamine and the aptamer-siRNA can be addeddirectly to the liquid environment of the cells. Lipid formulations canalso be administered to animals such as by intravenous, intramuscular,or intraperitoneal injection, or orally or by inhalation or othermethods as are known in the art. When the formulation is suitable foradministration into animals such as mammals and more specificallyhumans, the formulation is also pharmaceutically acceptable.Pharmaceutically acceptable formulations for administeringoligonucleotides are known and can be used. In some instances, it may bepreferable to formulate aptamer-siRNA in a buffer or saline solution anddirectly inject the formulated dsRNA into cells, as in studies withoocytes. The direct injection of dsRNA duplexes may also be done. Forsuitable methods of introducing siRNA see U.S. published patentapplication No. 2004/0203145 A1, incorporated herein by reference.

Suitable amounts of aptamer-siRNA must be introduced and these amountscan be empirically determined using standard methods. Typically,effective concentrations of individual aptamer-siRNA species in theenvironment of a cell will be about 50 nanomolar or less 10 nanomolar orless, or compositions in which concentrations of about 1 nanomolar orless can be used. In other embodiment, methods utilize a concentrationof about 200 picomolar or less and even a concentration of about 50picomolar or less can be used in many circumstances.

The method can be carried out by addition of the aptmer-siRNAcompositions to any extracellular matrix in which cells can liveprovided that the aptamer-siRNA composition is formulated so that asufficient amount of the aptamer-siRNA can enter the cell to exert itseffect. For example, the method is amenable for use with cells presentin a liquid such as a liquid culture or cell growth media, in tissueexplants, or in whole organisms, including animals, such as mammals andespecially humans.

Expression of a target gene can be determined by any suitable method nowknown in the art or that is later developed. It can be appreciated thatthe method used to measure the expression of a target gene will dependupon the nature of the target gene. For example, when the target geneencodes a protein the term “expression” can refer to a protein ortranscript derived from the gene. In such instances the expression of atarget gene can be determined by measuring the amount of mRNAcorresponding to the target gene or by measuring the amount of thatprotein. Protein can be measured in protein assays such as by stainingor immunoblotting or, if the protein catalyzes a reaction that can bemeasured, by measuring reaction rates. All such methods are known in theart and can be used. Where the gene product is an RNA species expressioncan be measured by determining the amount of RNA corresponding to thegene product. The measurements can be made on cells, cell extracts,tissues, tissue extracts or any other suitable source material.

The determination of whether the expression of a target gene has beenreduced can be by any suitable method that can reliably detect changesin gene expression. Typically, the determination is made by introducingthe aptamer-siRNA into the environment of a cell such that at least aportion of that aptamer-siRNA enters the cytoplasm and then measuringthe expression of the target gene. The same measurement is made onidentical untreated cells and the results obtained from each measurementare compared.

The aptamer-siRNA can be formulated as a pharmaceutical compositionwhich comprises a pharmacologically effective amount of an aptamer-siRNAand pharmaceutically acceptable carrier. A pharmacologically ortherapeutically effective amount refers to that amount of anaptamer-siRNA effective to produce the intended pharmacological,therapeutic or preventive result. The phrases “pharmacologicallyeffective amount” and “therapeutically effective amount” or simply“effective amount” refer to that amount of a RNA effective to producethe intended pharmacological, therapeutic or preventive result. Forexample, if a given clinical treatment is considered effective whenthere is at least a 20% reduction in a measurable parameter associatedwith a disease or disorder, a therapeutically effective amount of a drugfor the treatment of that disease or disorder is the amount necessary toeffect at least a 20% reduction in that parameter.

The phrase “pharmaceutically acceptable carrier” refers to a carrier forthe administration of a therapeutic agent. Exemplary carriers includesaline, buffered saline, dextrose, water, glycerol, ethanol, andcombinations thereof. For drugs administered orally, pharmaceuticallyacceptable carriers include, but are not limited to pharmaceuticallyacceptable excipients such as inert diluents, disintegrating agents,binding agents, lubricating agents, sweetening agents, flavoring agents,coloring agents and preservatives. Suitable inert diluents includesodium and calcium carbonate, sodium and calcium phosphate, and lactose,while corn starch and alginic acid are suitable disintegrating agents.Binding agents may include starch and gelatin, while the lubricatingagent, if present, will generally be magnesium stearate, stearic acid ortalc. If desired, the tablets may be coated with a material such asglyceryl monostearate or glyceryl distearate, to delay absorption in thegastrointestinal tract. The pharmaceutically acceptable carrier of thedisclosed dsRNA composition may be micellar structures, such as aliposomes, capsids, capsoids, polymeric nanocapsules, or polymericmicrocapsules.

Polymeric nanocapsules or microcapsules facilitate transport and releaseof the encapsulated or bound dsRNA into the cell. They include polymericand monomeric materials, especially including polybutylcyanoacrylate. Asummary of materials and fabrication methods has been published (seeKreuter, 1991). The polymeric materials which are formed from monomericand/or oligomeric precursors in the polymerization/nanoparticlegeneration step, are per se known from the prior art, as are themolecular weights and molecular weight distribution of the polymericmaterial which a person skilled in the field of manufacturingnanoparticles may suitably select in accordance with the usual skill.

Suitably formulated pharmaceutical compositions of this invention can beadministered by any means known in the art such as by parenteral routes,including intravenous, intramuscular, intraperitoneal, subcutaneous,transdermal, airway (aerosol), rectal, vaginal and topical (includingbuccal and sublingual) administration. In some embodiments, thepharmaceutical compositions are administered by intravenous orintraparenteral infusion or injection.

In general a suitable dosage unit of aptamer-siRNA will be in the rangeof 0.001 to 0.25 milligrams per kilogram body weight of the recipientper day, or in the range of 0.01 to 20 micrograms per kilogram bodyweight per day, or in the range of 0.01 to 10 micrograms per kilogrambody weight per day, or in the range of 0.10 to 5 micrograms perkilogram body weight per day, or in the range of 0.1 to 2.5 microgramsper kilogram body weight per day. Pharmaceutical composition comprisingthe aptamer-siRNA can be administered once daily. However, thetherapeutic agent may also be dosed in dosage units containing two,three, four, five, six or more sub-doses administered at appropriateintervals throughout the day. In that case, the aptamer-siRNA containedin each sub-dose must be correspondingly smaller in order to achieve thetotal daily dosage unit. The dosage unit can also be compounded for asingle dose over several days, e.g., using a conventional sustainedrelease formulation which provides sustained and consistent release ofthe aptamer-siRNA over a several day period. Sustained releaseformulations are well known in the art. In this embodiment, the dosageunit contains a corresponding multiple of the daily dose. Regardless ofthe formulation, the pharmaceutical composition must containaptamer-siRNA in a quantity sufficient to inhibit expression of thetarget gene in the animal or human being treated. The composition can becompounded in such a way that the sum of the multiple units ofaptamer-siRNA together contain a sufficient dose.

Data can be obtained from cell culture assays and animal studies toformulate a suitable dosage range for humans. The dosage of compositionsof the invention lies within a range of circulating concentrations thatinclude the ED₅₀ (as determined by known methods) with little or notoxicity. The dosage may vary within this range depending upon thedosage form employed and the route of administration utilized. For anycompound used in the method of the invention, the therapeuticallyeffective dose can be estimated initially from cell culture assays. Adose may be formulated in animal models to achieve a circulating plasmaconcentration range of the compound that includes the IC₅₀ (i.e., theconcentration of the test compound which achieves a half-maximalinhibition of symptoms) as determined in cell culture. Such informationcan be used to more accurately determine useful doses in humans. Levelsof dsRNA in plasma may be measured by standard methods, for example, byhigh performance liquid chromatography.

The practice of the present invention employs, unless otherwiseindicated, conventional techniques of chemistry, molecular biology,microbiology, recombinant DNA, genetics, immunology, cell biology, cellculture and transgenic biology, which are within the skill of the art.See, e.g., Maniatis et al., 1982, Molecular Cloning (Cold Spring HarborLaboratory Press, Cold Spring Harbor, N.Y.); Sambrook et al., 1989,Molecular Cloning, 2nd Ed. (Cold Spring Harbor Laboratory Press, ColdSpring Harbor, N.Y.); Sambrook and Russell, 2001, Molecular Cloning, 3rdEd. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.);Ausubel et al., Current Protocols in Molecular Biology (John Wiley &Sons, including periodic updates, 2008); Glover, 1985, DNA Cloning (IRLPress, Oxford); Russell, 1984, Molecular biology of plants: a laboratorycourse manual (Cold Spring Harbor Laboratory Press, Cold Spring Harbor,N.Y.); Anand, Techniques for the Analysis of Complex Genomes, (AcademicPress, New York, 1992); Guthrie and Fink, Guide to Yeast Genetics andMolecular Biology (Academic Press, New York, 1991); Harlow and Lane,1988, Antibodies, (Cold Spring Harbor Laboratory Press, Cold SpringHarbor, N.Y.); Nucleic Acid Hybridization (B. D. Hames & S. J. Higginseds. 1984); Transcription And Translation (B. D. Hames & S. J. Higginseds. 1984); Culture Of Animal Cells (R. I. Freshney, Alan R. Liss, Inc.,1987); Immobilized Cells And Enzymes (IRL Press, 1986); B. Perbal, APractical Guide To Molecular Cloning (1984); the treatise, Methods InEnzymology (Academic Press, Inc., N.Y.); Methods In Enzymology, Vols.154 and 155 (Wu et al. eds.), Immunochemical Methods In Cell AndMolecular Biology (Mayer and Walker, eds., Academic Press, London,1987); Handbook Of Experimental Immunology, Volumes I-IV (D. M. Weir andC. C. Blackwell, eds., 1986); Riott, Essential Immunology, 6th Edition,Blackwell Scientific Publications, Oxford, 1988; Fire et al., RNAInterference Technology: From Basic Science to Drug Development,Cambridge University Press, Cambridge, 2005; Schepers, RNA Interferencein Practice, Wiley-VCH, 2005; Engelke, RNA Interference (RNAi): The Nuts& Bolts of siRNA Technology, DNA Press, 2003; Gott, RNA Interference,Editing, and Modification: Methods and Protocols (Methods in MolecularBiology), Human Press, Totowa, N. J., 2004; Sohail, Gene Silencing byRNA Interference: Technology and Application, CRC, 2004.

EXAMPLES

The present invention is described by reference to the followingExamples, which are offered by way of illustration and are not intendedto limit the invention in any manner. Standard techniques well known inthe art or the techniques specifically described below were utilized.

Example 1 Materials and Methods for Examples 2-7

Materials: Unless otherwise noted, all chemicals were purchased fromSigma-Aldrich, all restriction enzymes were obtained from New EnglandBioLabs (NEB) and all cell culture products were purchased from GIBOC(Gibco BRL/Life Technologies, a division of Invitrogen.).

siRNAs: siRNA and antisense strand RNA were purchased from IntegratedDNA Technologies (IDT). Anti-tat/rev 27 mer siRNA: Sense sequence:5′-GCGGAGACAGCGACGAAGAGCUCAUCA-3′ (SEQ ID NO:10); Antisense:5′-UGAUGAGCUCUUCGUCGCUGUCUCCGCdTdT-3′ (SEQ ID NO:2); Anti-tat/rev 21 mersiRNA: Sense sequence: 5′-GCGGAGACAGCGACGAAGAGC-3′ (SEQ ID NO:11);Antisense: 5′-GCUCUUCGUCGCUGUCUCCGCdTdT-3′ (SEQ ID NO:3).

Aptamer-siRNA chimeras: The 27 or 21 mer sense strand is marked in bold,the linker (CUCU) is indicated in italics and mutated nucleotides areunderlined. Aptamer:5′-GGGAGACAAGACUAGACGCUCAAUGUGGGCCACGCCCGAUUUUACGCUUUUACCCGCACGCGAUUGGUUUGUUUCCC-3′(SEQ ID NO:12). Ch L-1 sense strand:5′-GGGAGACAAGACUAGACGCUCAAUGUGGGCCACGCCCGAUUUUACGCUUUUACCCGCACGCGAUUGGUUUGUUUCCCCUCUGCGGAGACAGCGACGAAGAGCUCAUCA-3′(SEQ ID NO:1). Ch 1 sense strand:5′-GGGAGACAAGACUAGACGCUCAAUGUGGGCCACGCCCGAUUUUACGCUUUUACCCGCACGCGAUUGGUUUGUUUCCCGCGGAGACAGCGACGAAGAGCUCAUCA-3′(SEQ ID NO:13). Ch L-2 sense strand:5′-GGGAGACAAGACUAGACGCUCAAUGUGGGCCACGCCCGAUUUUACGCUUUUACCCGCACGCGAUUGGUUUGUUUCCCCUCUGCGGAGACAGCGACGAAGAGC-3′(SEQ ID NO:14). Ch 2 sense strand:5′-GGGAGACAAGACUAGACGCUCAAUGUGGGCCACGCCCGAUUUUACGCUUUUACCCGCACGCGAUUGGUUUGUUUCCCGCGGAGACAGCGACGAAGAGC-3′(SEQ ID NO:15). M-1 sense strand:5′-GGGAGACAAGACUAGACGCUCAAUGUGGGCGGGGCCCGAUUUUACCGUUUUCAAAGCACGCGAUUGGUUUGUUUCCCCUCUGCGGAGACAGCGACGAAGAGCUCAUCA-3′(SEQ ID NO:16). M-2 sense strand:5′-GGGAGACAAGACUAGACGCUCAAUGUGGGCCACGCCCGAUUUUACGCUUUUACCCGCACGCGAUUGGUUUGUUUCCCCUCUGCGGAGACAGCGUGUAAGAGCUCAUCA-3′ (SEQ ID NO:17). Ch L-1, Ch1 and M-1 antisense strand:5′-UGAUGAGCUCUUCGUCGCUGUCUCCGCdTdT-3′ (SEQ ID NO:2). Ch L-2, Ch 2antisense strand: 5′-GCUCUUCGUCGCUGUCUCCGCdTdT-3′ (SEQ ID NO:3). M-2antisense strand: 5′-UGAUGAGCUCUUACACGCUGUCUCCGCdTdT-3′ (SEQ ID NO:18).

Generation of aptamer and chimera RNAs by in vitro transcription:Double-stranded DNA templates were directly generated by PCR and theresulting PCR products were recovered using a QIAquick Gel purificationKit. Chimera sense strands were transcribed from its PCR generated DNAtemplates using the DuraScription Kit (Epicentre, Madison, Wis.)according to the manufacturer's instruction. In the transcriptionreaction mixture, the canonical CTP and UTP were replaced with 2′-F-CTPand 2′-F-UTP to produce RNA that is resistant to RNase A degradation.The reactions were incubated at 37° C. for 6 h, and subsequentlypurified with Bio-Spin 30 Columns (Bio-Rad) following phenol extractionand ethanol precipitation. RNA was treated by CIP to remove theinitiating 5′-triphosphate. To prepare the chimeras, the chimerasharboring only the sense strand RNA was combined with the appropriateantisense RNA in HBS buffer (10 mM HEPES pH 7.4, 150 mM NaCl, 1 mMCaCl₂, 1 mM MgCl₂, 2.7 mM KCl), heated to 95° C. for 3 mM and thencooled to 37° C. slowly. Incubation continued at 37° C. for 10 min.Fluorescent aptamer and chimeras were generated using the Silencer siRNALabeling Kit (Ambio) according to the manufacturer's instructions.

Cell Culture: HEK 293 cells and CEM cells were purchased from ATCC andcultured in DMEM and RPMI 1640 supplemented with 10% FBS respectively,according to their respective data sheets. CHO-WT and CHO-EE cells wereobtained through the AIDS Research and Reference Reagent Program,Division of AIDS, NIAID, NIH. They are grown in GMEM-S. Cells werecultured in a humidified 5% CO₂ incubator at 37° C.

Cell-surface binding of aptamer-siRNA chimeras (flow cytometryanalysis): CHO-gp160 or CHO-EE cells were washed with PBS, trypsinizedand detached from the plates. After washing cells twice times with 500μL of binding buffer (10 mM HEPES pH 7.4, 150 mM NaCl, 1 mM CaCl₂, 1 mMMgCl₂, 2.7 mM KCl, 0.01% BSA). Cell pellets were resuspended in bindingbuffer and incubated at 37° C. for 30 mM. Cells were then pelleted andresuspended in 50 μL of binding buffer (prewarmed to 37° C.) containingeither 400 nM Cy3-labeled aptamer or Chimera RNAs. After incubation at37° C. for 40 min, cells were washed three times with 500 μL of bindingbuffer prewarmed to 37° C., and finally resuspended in 350 μL of bindingbuffer prewarmed to 37° C. and analyzed by flow cytometry.

Cellular binding and uptake studies (confocal microscopy analysis): TheCHO-gp160 and CHO-EE cells lines were grown in 8-well chambered-slidewith seeding at 1×10⁵ in GMEM-S medium to allow 50%-70% confluence in 24h. On the day of experiments, cells were washed with 250 μL of prewarmedPBS. And incubated with 250 μL of prewarmed completely growth medium for30 min at 37° C. Cy3-labeled RNAs at 20 nM of final concentration wereadded into the media and incubated at 37° C. for 1.5 hrs. Subsequently,cells were washed three times with 250 μL of prewarmed PBS, fixed with4% formaldehydes for 10 min. The cells were stained by treatment with100 μL of Vybrant Cell-Labeling Solution (DIO membrane dye, MolecularProbes, Invitrogen) according to the manufacturer's instructions. Theimages were collected using a Zeiss LSM 510 upright 2 photon confocalmicroscopy system under water immersion at 40 magnifications. Imageswere combined and deconvoluted to reconstruct a three-dimensional image.

Analysis of chimera processing: Sense RNAs were annealed with equalmoles of 5′-end-labeled antisense strands in HBS buffer in order to formchimeric dsRNA. The chimeras or dsRNAs were incubated at 10 nM of finalconcentration in the absence of target mRNA in HCT116 cell lysates forvarying times (20 min, 60 min and 120 min) Reactions were stopped byphenol/chloroform extraction and the RNAs were collected forelectrophoresis in a denaturing 20% polyacrylamide gel. The gels weresubsequently dried and exposed to X-ray film.

Dual luciferase assays: (Day 1) CHO-gp160 and CHO-EE cells weretransfected with pNL4-3. Luc.R-.E- (NIH AIDS Research and ReagentProgram, Germantown, Md.) and pRSV-Renilla using Lipofectamine 2000(Invitrogen) according to the manufacturer's instructions.pNL4-3.Luc.R-.E- is an Env- Vpr- non-infectious clone containing thefirefly luciferase (F-Luc) gene inserted into the nef gene. (Day 2)Cells which transiently expressed pNL4-3.Luc were seeded in 24-wellplates at 50-70% confluency. For siRNA, (Day 3) cells were transfectedwith 200 nM RNA using Lipofectamine 2000. For aptamer-mediated siRNAdelivery, (Day 3) cells were incubated in 400 μL refresh complete growthmedia for 30 min at 37° C. The chimeras RNAs were added directly to themedia (400 μL) at a final concentration of 200 nM chimeras. Cells wereharvested for analysis on day 4. The expression of the pNL4-3.Luc andnormalizing control Renilla luciferase were detected by theDual-luciferase Reporter Assay System (Promega, USA) according to themanufacturer's instructions. All samples were transfected in triplicateand the experiment was performed a minimum of three times.

5′-RACE PCR assay: Total RNA (5 μg) from CHO-gp160 cells treated withdifferent siRNAs and chimeras was ligated to a GeneRacer adaptor(Invitrogen) without prior treatment. Ligated RNA was reversedtranscribed using a gene specific primer 1 (GSP-Rev 1:5′-TCACCCTCTCCACTGACAGAGAACTT-3′ (SEQ ID NO:19)). To detect cleavageproducts, PCR was preformed using primers complementary to the RNAadaptor (5′-cDNA primer: 5′-GGACACTGACATGGACTGAAGGAGTA-3′ (SEQ IDNO:20)) and gene-specific primer 2 (GSP-Rev 2:5′-TAACCTCTCAAGCGGTGGTAGCTGAA-3′ (SEQ ID NO:21)). Amplification productswere resolved by agarose gel electrophoresis and visualized by ethidiumbromide staining. The identity of the specific PCR products wasconfirmed by sequencing of the excised bands.

Northern blot analysis: CEM cells were infected by HIV NL4-3 for 10days. Prior to adding the various RNAs, the infected-CEM cells weregently washed 3 times to clear out free virus. 5×10⁴ cells wereincubated with refolded RNAs at 400 nM final concentrations in 96-wellplates at 37° C. The total RNAs were harvested on the 7^(th) day postapplication for analysis with STAT-60 (TEL-TEST “B”, Friendswood, Tex.)according to the manufacturer's instructions. Two micrograms of totalRNAs were electrophoresed in a 15% polyacrylamide-8 M urea gel and thentransferred to a Hybond N+ membrane (Amersham pharmacia Biotech, USA).Prehybridization and hybridization were carried out using PerfectHybPlus Hybridization buffer (Sigma, USA) at 37° C. with 3 pmol of a 27-merDNA oligonucleotide probe end-labeled with T4 polynucleotide kinase andγ-P³²-ATP. Filters were washed three times at 37° C. for 15 min, priorto autoradiography. We also probed for human U6 snRNA as an internal RNAloading standard.

qRT-PCR analysis: CEM cells were infected with HIV NL4-3 for 10 days.Prior to analyses, the infected-CEM cells were gently washed three timesto eliminate free virus. The infected CEM cells were treated directlywith the aptamer or Ch L-1 at 400 nM of final concentration. After 7 d,total RNAs were isolated with STAT-60 (TEL-TEST “B”, Friendswood, Tex.).Expression of the tat/rev coding RNAs was analyzed by quantitativeRT-PCR using 2×iQ SyberGreen Mastermix (BIO-RAD) and specific primersets at a final concentration of 400 nM. Primers were as follows:tat/rev forward primer: 5′-GGCGTTACTCGACAGAGGAG-3′ (SEQ ID NO:22);tat/rev reverse primer: 5′-TGCTTTGATAGAGAAGCTTGATG-3′ (SEQ ID NO:23);GAPDH forward primer: 5′-CATTGACCTCAACTACATG-3′ (SEQ ID NO:24); GAPDHreverse primer: 5′-TCTCCATGGTGGTGAAGAC-3′ (SEQ ID NO:25).

RNA-Stat60 was used to extract total RNA according to the manufacturer'sinstruction (Tel-Test). Residual DNA was digested using the DNA-free kitper the manufacturer's instructions (Ambion). cDNA was produced using 2μg of total RNA Moloney murine leukemia virus reverse transcriptase andrandom primers in a 15 μL reaction according to the manufacturer'sinstructions (Invitrogen). GAPDH expression was used for normalizationof the qPCR data.

HIV-1 challenges and p24 antigen assay: Method 1: NL4-3 virus wasincubated with refolded RNAs at 37° C. for 1 h. Subsequently, viruseswere gently washed with PBS and used to infect CEM cells. The culturesupernatants were collected at different time post infection (7 d, 11 d,15 d and 18 d) for p24 antigen analyses. Method 2: CEM cells wereinfected with HIV NL4-3 for 10 days. Prior to RNA treatments theinfected-CEM cells were gently washed with PBS three times to eliminatefree virus. 1.5×10⁴ infected CEM cells and 3.5×10⁴ uninfected CEM cellswere incubated with refolded RNAs at 400 nM of final concentration in96-well plates at 37° C. The culture supernatants were collected atdifferent time (3 d, 5 d, 7 d and 9 d). The p24 antigen analyses wereperformed using a Coulter HIV-1 p24 Antigen Assay (Beckman Coulter)according to the manufacturer's instructions.

Interferon assay (qRT-PCR Analysis): For HEK293 cells, the cells weretransfected with siRNA and chimeras RNAs (50 nM) or 200 ng poly(IC)using lipofectamine 2000 (Invitrogene). For infected CEM cells, cellswere directly treated with chimera RNAs (400 nM) or IFN-alpha (100U/mL). After 24 h, total RNAs were isolated with STAT-60 (TEL-TEST “B”,Friendswood, Tex.). Expression of human mRNAs encoding IFN-β, p56(CDKL2) and OAS 1 were analyzed by quantitative RT-PCR using 2× iQSyberGreen Mastermix (BIO-RAD) as described above and specific primersets for these genes at final concentrations of 400 nM. Primers were asfollows: IFN-β forward, 5′-AGACTTACAGGTTACCTCCGAA-3′ (SEQ ID NO:26);IFN-β reverse, 5′-CAGTACATTCGCCATCAGTCA-3′ (SEQ ID NO:27); P56 forward,5′-GCCTCCTTGGGTTCGTCTATAA-3′ (SEQ ID NO:28); P56 reverse,5′-CTCAGGGCCCGCTCATAGTA-3′ (SEQ ID NO:29); OAS 1 forward,5′-GGAGGTTGCAGTGCCAACGAAG-3′ (SEQ ID NO:30); OAS 1 reverse,5′-TGGAAGGGAGGCAGGGCATAAC-3′ (SEQ ID NO:31).

Example 2 Design of Anti-gp120 Aptamer-siRNA Chimeras

Anti-120 aptamer-siRNA chimeras were designed for cell-specific deliveryand siRNA processing. To enhance the stability of the chimeric RNAs incell culture and in vivo (4, 34-37), the aptamer and sense strandsegment of the siRNAs contained nuclease-resistant 2′-Fluoro UTP and2′-Fluoro CTP and were synthesized from corresponding dsDNA templates byin vitro bacteriophage transcription (FIG. 1). To prepare the siRNAcontaining chimeras, in vitro transcribed chimeric aptamer-sense strandpolymers were annealed with equimolar concentrations of an unmodifiedantisense strand RNA. These 2′-Fluoro modified chimeras were stable incell-culture media for up to 48 hours whereas the unmodified controlRNAs were quickly degraded within several minutes (data not presented).

The gp120-binding aptamer which neutralizes R5 strains of HIV-1 has beenpreviously described and characterized (31). Since the synthetic Dicersubstrate duplexes of 25-30 nt have been shown to enhance RNAi potencyand efficacy, we chose a 27 mer duplex RNA as the siRNA portion of ourchimeric molecule. The 27 mer siRNA portion of chimeras (Ch L-1 andCh 1) targets the HIV-1 tat/rev common exon sequence. The chimerasdesigned Ch L-2 and Ch 2 are identical to Ch L-1 and Ch 1 with theexception that the 27 mer duplex is replaced by a 21 base pair duplex.In the Ch L-1 and Ch L-2 designs we inserted a four nucleotide linker(CUCU) between the aptamer and siRNA portions to minimize stericinterference of the aptamer portion with Dicer. Previous studies on theanti-gp120 aptamer identified the minimal region of the aptameressential for binding gp120 and showed mutations within this regionsignificantly lower the binding affinity. As controls for aptamerbinding we created the chimera designated as M-1. As a control for thesiRNA mediated silencing we constructed an additional mutant in thesiRNA portion which should abrogate RNAi directed cleavage of thetarget, and this is designated as M-2.

Because of competition by the sense (passenger) strand with theanti-sense (guide) strand for RISC entry, the strand selectivity is animportant factor for evaluating siRNAs. Therefore, we evaluated thesechimeras RNA using the SiCheck reporter system, which readily allowsscreening of the potencies of candidate sh/siRNAs. The gene silencing ofboth the sense target (corresponding to the mRNA) and the anti-sensetarget were tested independently and the selectivity ratios could becalculated as a measure of the relative incorporation of each strandinto the RISC. The comparison (FIG. 7) demonstrated that the Ch L-1mediated ˜86% knockdown of the sense target; however, knockdown of theanti-sense target is much less (˜50%), indicative of good strandselection (R=3.2). Ch 1 also indicated similar knockdown (˜83%) of thesense target and strand selection (R=2.9). In contrast, Ch L-2 and Ch 2have poorer efficacy (<70%) and strand selectivity (R=1.9 and 1.6,respectively). These data suggest that the aptamer-27 mer siRNA chimerasindeed enhance the RNAi efficacy and potent, consistent with previousstudies in our laboratory (29, 30).

Example 3 Anti-gp120 Aptamer-siRNA Chimeras Bind and are Internalized byCells Expressing HIV gp160

We found that anti-gp120 aptamer-siRNA chimeras bind and areinternalized by cells expressing HIV gp160. CHO-gp160 cells stablyexpressing the HIV envelope glycoprotein gp160 were used to test uptakeof the chimeric aptamer-siRNAs. These cells do not process gp160 intogp120 and gp41 since they lack the gag encoded proteases required forenvelope processing. As a control we used the parental CHO-EE cell linewhich does not express gp160. The anti-gp120 aptamer and the chimeraswere labeled with Cy3 to follow their binding and potentialinternalization in gp160 expressing cells. Flow cytometric analyses(FIG. 2A) revealed that the aptamer and chimeras specifically bound tothe CHO-gp160 cells but did not bind to the control CHO-EE cells. Asanticipated, the M-1 dramatically reduced binding to the CHO-gp160expressing cells.

In order to determine if the bound aptamer and chimeras wereinternalized in the gp160 expressing cells, we carried out Z-axisconfocal microscopy and three-dimensional image reconstruction with theCHO-gp160 cells incubated with the Cy3-labeled transcripts. Both theanti-gp120 aptamer (data not presented) and Ch 1 (FIG. 2B) wereselectively internalized within the CHO-gp160 cells but not the CHO-EEcontrol cells. The M-1 was also not internalized. Three-dimensionalimage reconstruction (FIG. 8) shows localization of the Cy3-labeled Ch 1in a single cell. To visualize the plasma membranes the cells werestained with the carbocyanine dye DIO.

Example 4 Anti-gp120 Aptamer-siRNA Chimeras are Processed by Dicer

We next asked whether or not the siRNAs could be processed from thechimeras by Dicer in whole cell extracts that contain good Dicercleavage activity. The first set of experiments used a 5′-end P³²labeled antisense strand to follow Dicer processing (FIG. 3A). The sizeof the P³² labeled cleavage product(s) indicates from which directionDicer enters the siRNA and cleaves. When Ch L-1 was incubated with thecytoplasmic lysate, we observed that the 27 nt antisense strand wasprocessed into a 21-23 nt siRNA (FIG. 3B). This result suggests Dicerprocessing preferentially enters from the 5′ end of the antisense strandand cleaves 21 to 23 nt downstream, leaving the 5′ end of the antisensestrand intact. In contrast, the 21 base siRNAs were not processedfurther in these extracts.

Example 5 Anti-gp120 Aptamer-siRNA Chimeras Specifically Silence TargetGene Expression

To evaluate whether these anti-gp120 aptamer-siRNA chimeras function intriggering RNAi, we first transfected CHO-gp160 and CHO-EE cells withHIV pNL4-3 Luc. The HIV pNL4-3 has the firefly luciferase under thecontrol of the HIV LTR and is Tat responsive. The anti-tat/rev siRNAefficacy is monitored by inhibition of luciferase expression. Subsequentto the transfections the cells were treated with the chimeras in theabsence or presence of the transfection reagent Lipofectamine 2000.

Luciferase expression was potently inhibited when Ch L-1 and Ch 1 werelipofected into both types of cells (FIG. 4A). However, in the absenceof lipofection, gene silencing from Ch L-1 and Ch 1 was specific toCHO-gp160 expressing cells and no inhibition of luciferase was observedin CHO-EE cells. Interestingly, Ch L-1 and Ch 1 which are linked to the27 mer duplex RNA showed somewhat greater efficacy than Ch L-2 and Ch 2,consistent with our previous observations of Dicer substrates enhancingRNAi (29, 30).

To validate that the siRNAs released from the chimeras were triggeringRNAi we transfected CHO-gp160 cells with a Rev-EGFP fusion constructharboring the siRNA targets. The transfected cells were then transfectedwith Ch L-1, Ch L-2, 27 mer siRNA or 21 mer siRNA in presence ofLipofectamine 2000. Thirty six hours post transfection total RNA wasisolated and subjected to a modified 5′-RACE (Rapid amplification ofcDNA ends) technique to identify the specific cleavage products in theRev portion of the fusion transcript. We assumed that the Ago2 mediatedcleavage was between bases 10 and 11 relative to the 5′ end of eachsiRNA. Our Dicer analyses of the 27 mer revealed that it is cleaved21-23 nucleotides downstream from the 5′ end of the antisense strand(antisense relative to the tat/rev target), whereas the 21 mer is notprocessed further (FIG. 3B). We expected that the RNAi mediated cleavagesite in the target would be shifted by six bases between the 27 mer andthe 21 mer derived siRNAs. Fragments of the predicted lengths wereobtained from cells treated with the siRNAs or chimeras (FIG. 4B).Direct sequencing of the excised bands verified the expected PCRproduct, which demonstrated that cleavage occurred at the predictedposition for the siRNA duplex between positions 10 and 11 from the 5′end of the siRNA antisense strand (FIG. 9). These data provide a formaldemonstration that the chimeras produce siRNAs that are incorporatedinto RISC. As expected, no RACE PCR products were generated from RNAisolated from cells untreated with the chimeras or siRNAs.

Example 6 Anti-gp120 Aptamer-siRNA Chimeras Inhibit HIV gp120 MediatedCell Fusion and HIV-1 Infection of CEM-T Cells

Essential to the use of the aptamer-siRNA chimeras in treating HIVinfection is that the aptamer allows internalization of the chimeras inHIV infected cells. We first demonstrated by Northern blot analyses thatchimeric delivered siRNAs were detectable in HIV infected CEM cellsdirectly which were treated with the chimeras. The Northern blottingdata of FIG. 5A demonstrate that the siRNAs from chimera areinternalized in HIV infected CEM cells since the 27 mer was processed to21-23 base siRNAs in these cells, but not in the gp120-negativeuninfected CEM cells, suggesting that the chimeras specificallydelivered siRNA into the infected CEM cells through anti-gp120 aptamer.As expected, the 21 or 27 mer duplex siRNAs in absence of the aptamerswere not detectable in the CEM cells owing to the lack ofinternalization (FIG. 5A). Since a little of non-specific bindingsexisted on the cells surface, tiny 21 or 27 mer RNA from chimeras (ChL-1, Ch 1 and Ch L-2) also were hybridized in uninfected CEM.

To further confirm siRNA function after internalization to infected CEMcells, qRT-PCR was preformed to evaluate the tat/rev gene expression.Aptamer or chimeras were added directly to media containing infected CEMcells. After 7 days, treated cells were harvested, the total RNA wasextracted and the extent of tat/rev gene inhibition was determined byquantitative RT-PCR expression assays. We find that the treatment ofinfected CEM cells with the chimeras is able to induce silencing of thetat/rev gene, while the aptamer alone did not affect tat/rev geneexpression (FIG. 5B). These results provide further support that thechimeric delivered siRNA triggers RNAi.

In HIV-1 infection, gp120 expressed at the cell surface will inducesyncytia formation between infected and uninfected cells due tointeractions between gp120 and CD4 (27, 28). We therefore sought todetermine if the aptamer and chimeras would have an impact on syncitiaformation in cell culture. In this assay, the HIV-1 infected-CEM cellswere incubated with siRNA or chimeras RNAs. Subsequently, the uninfectedMT2 cells expressing CD4 were added into infected-CEM cells treated withRNA. After 48 h of co-incubation at 37° C., cells syncytia were analyzedmicroscopically. The treatment of the HIV infected cultures with theaptamer and chimeras resulted in a clear reduction in syncytia formation(Data not presented). We also asked if the aptamer and chimeras preventHIV replication in an acute infection assay by monitoring HIV-1 Gag p17via an immunofluorescence assay (IF) (FIG. 10). These assays revealed amarked reduction in p17 expression in the HIV infected cells treatedwith the anti-gp120 aptamer and even more pronounced reduction with theCh L1 chimera.

To further verify the activity of the anti-HIV activity of the chimerasin inhibition of HIV-1 replication, we carried out the following assays.In the first assay, HIV-1 was first mixed with the chimeras or aptamerand subsequently the viruses were used to infect CEM cells. In thisassay the infectivities of the aptamer or chimera treated virus weresignificantly reduced and viral replication was suppressed out to twoweeks (FIG. 5C). Ch L-1 was the most effective inhibitory agent. In thesecond experiment, the aptamer or chimeras were incubated with HIVinfected-CEM cells. At different days post treatment with the aptamerand chimeras, aliquots of the media were assayed for viral p24 antigenlevels. The results of these analyses (FIG. 5D) showed that all of theaptamer containing RNAs inhibited p24 production, but the strongestinhibition was observed with Ch L-1 treatment, again consistent with ourresults from the other assays. These data, together with the inhibitionof cell fusion and p17 expression, demonstrate that the anti-gp120aptamer-siRNA chimera system can strongly inhibit HIV-1 replication andinfection. Moreover, the suppression is attributed to the combinedaffect of the aptamer binding gp120 and RNAi.

Example 7 Anti-gp120 Aptamer-siRNA Chimeras do not Trigger an InterferonResponse

It has been reported previously that siRNAs delivered by liposomes orpolyplex reagents can non-specifically activate inflammatory cytokineproduction (TNFα, IL-6 and IL-12) as well as IFN responsive genes, whichin turn can trigger cellular toxicity (38-40). We therefore assessed theinduction of type I interferon regulated gene expression by ouranti-gp120 aptamer-siRNA chimeras using quantitative RT-PCR expressionassays. As a positive control, we incubated the target cells withpoly(IC). We find that the treatment of HEK293 cells with the chimerasdid not significantly induce expression of the interferon-β and p56genes (FIG. 6A). Since CEM cells are difficult to be transfected withcontrol molecules such as poly (IC), we used IFN-α as a positive controlto confirm upregulation of p56 and OAS1 gene expression. As we observedin the HEK293 transfection assays, treatment of CEM cells with thechimeras did not induce type I IFN responses (FIG. 6B). Similar resultswere obtained using HIV infected CEM cells treated with the chimeras,suggesting that the gp120 mediated internalization of the chimeras doesnot trigger toxic IFN responses.

Example 8 Discussion of Examples 1-7

Aptamers are nucleic acid species that have been engineered throughrepeated rounds of in vitro selection to bind to various moleculartargets such as small organic molecules, proteins, nucleic acids, andeven cells (41-43). Because aptamers are capable of binding with highspecificity to their ligands at low nano- to picomolar dissociationconstants they can be used as molecular drugs for both basic researchand clinical purposes (44-48).

The success of RNAi-based clinical applications is dependent upon theefficiency of siRNA delivery to target cells. In this report, we havecapitalized upon the exquisite specificity of a gp120 aptamer to deliveranti-HIV siRNAs into HIV infected cells with the net result thatreplication and spread of HIV is strongly inhibited by the combinedaction of the aptamer and siRNA targeting the tat/rev common exon ofHIV-1.

We utilized the HIV-1 envelop protein gp120 as a model receptor fortargeted intracellular delivery of anti-HIV siRNAs. Cell type-specificbinding and uptake of chimeric aptamer-siRNA conjugates were achievedthrough the interaction of the aptamer portion with gp120 on the cellsurface of infected cells. To insure the stability of our RNA chimericmolecules in sera, we utilized the RNA stabilizing 2′-Fluoro backbonemodifications of pyrimidines on the aptamer and siRNA sense strand. Theantisense strand was not chemically modified, but was in fact stabilizedby virtue of its base pairing to the modified sense strand.

Notably, the cell type-specific gene silencing revealed that the siRNAswere successfully delivered into cells and entered into the RNAi pathwayby interaction of the anti-gp120 aptamer with gp120 expressed on thecell surface. Interestingly, the chimeras containing a 27 mer duplex RNAgave better efficacy in gene silencing than the corresponding 21 merduplex containing chimeras. The 27 mer duplex alone was also more potentthan the 21 mer duplex when these RNAs were delivered by lipofection. Weattribute this increased potency to Dicer processing of the 27 merwherein the processed 21-23 mer siRNAs are more readily handed off toRISC. It is of interest that we never observed complete processing ofthe 27 mer into 21-23 mers in our Northern Blot analyses of cellstreated with the chimeras. This may in part be a consequence of the highintracellular concentrations achieved by aptamer delivery, but may alsoreflect that the design of our blunt ended duplexes is sub-optimal forDicer processing. We observed that rather than enter the duplex from the2 base 3′ overhang, Dicer cleavage initiated following entry onto theduplex from the blunt end of the duplex. To this end we are testingother structures of the siRNA portion of the aptamers to achieve morecomplete Dicing.

An interesting observation is that analyses of the target cleavageproducts by a 5′-RACE technique further demonstrated that neither the 27mer nor 21 mer siRNAs underwent processing to trigger duplexes with twobase 3′ overhangs on both ends of the siRNAs. In fact for both the 21mer and 27 mer derived siRNAs, the target mRNA was cleaved betweenpositions 10 and 11 relative to the blunt 5′ end of the siRNA antisensestrand. These results suggest that unprocessed 27 mer as well as Dicerprocessed 27 mer antisense strands may be incorporated into RISC. Giventhe results from the cell extract Dicing reaction, which revealed thatthe 27 mer is not processed at the 5′ end of the antisense but only atthe 3′ end, it is not possible to determine whether all, some or none ofthe activated RISC was derived from intact 27 mer antisense gettingincorporated directly into RISC.

Aptamers that bind to viral or cellular proteins with high affinity andspecificity are useful for therapeutic applications. In this study, bothaptamer and chimeras can dramatically suppress the replication andproduction of HIV-1 in a variety of assays. These results demonstrateimportant attributes of the anti-gp120 aptamer as both inhibitors of HIVvia direct binding to virion or intracellular gp120 and as a cell typespecific delivery vector for therapeutic siRNAs.

Because the anti-gp120 aptamer is responsible for the targeted deliveryof siRNAs, gp120 expression is necessary for cell type-specifictransport. This is in essence a safety feature which could becapitalized upon to deliver siRNAs that target HIV or even cellularmessages essential for viral replication. Since only HIV infected cellswould bear the inhibitory action of the siRNA, this approach greatlyminimizes potential off-target effects by the siRNAs.

The dual inhibitory potential of the aptamer-siRNA fusion is animportant point of discussion. Both the aptamer and chimeras showedstrong inhibition of syncitial cell formation, expression of HIV-1 Gagp17 and HIV replication and spreading in HIV-1 infected-CEMT-lymphocytes. The anti-gp120 aptamer neutralizes HIV-1 infectivity viablocking the interaction of gp120 and CD4, and the siRNA silencestat/rev expression. Thus, the anti-gp120/HIV chimeras serve adouble-function and therefore provide greater efficacy than either theaptamer or siRNA applied alone. Finally, we show that the aptamermediated delivery of siRNAs via binding to gp120 and subsequentinternalization does not trigger type I interferon gene responses indifferent cell lines.

In summary, this strategy provides a new paradigm for delivery ofanti-HIV siRNAs by allowing selective delivery to HIV infected cells anddual function inhibition of HIV replication and spread. Moreover, theaptamer and siRNAs can be readily changed to accommodate genetic changesin the virus, making, making this an attractive approach for systemicanti-HIV therapy.

Example 9 Materials and Methods for Example 10

Generation of Aptamer and Chimera RNAs by In Vitro Transcription:

Aptamer and chimeras RNA were prepared as described above. Specially,the sense strands of aptamer-siRNA chimeras were underlined. The italicUU was the linker between the aptamer portion and siRNA portion. A-1aptamer:5′-GGGAGGACGAUGCGGAAUUGAGGGACCACGCGCUGCUUGUUGUGAUAAGCAGUUUGUCGUGAUGGCAGACGACUCGCCCGA-3′(SEQ ID NO:8); B-68 aptamer:5′-GGGAGGACGAUGCGGACAUAGUAAUGACACGGAGGAUGGAGAAAAAACAGCCAUCUCUUGACGGUCAGACGACUCGCCCGA-3′(SEQ ID NO:9); Chimera A-1-sense strand:5′-GGGAGGACGAUGCGGAAUUGAGGGACCACGCGCUGCUUGUUGUGAUAAGCAGUUUGUCGUGAUGGCAGACGACUCGCCCGAUUGCGGAGACAGCGACGAAGAGCUCAUCA-3′(SEQ ID NO:32); Chimera B-68-sense strand:5′-GGGAGGACGAUGCGGACAUAGUAAUGACACGGAGGAUGGAGAAAAAACAGCCAUCUCUUGACGGUCAGACGACUCGCCCGAUUGCGGAGACAGCGACGAAGAGCUCAUCA-3′(SEQ ID NO:33); Antisense strand: 5′-UGAUGAGCUCUUCGUCGCUGUCUCCGCdTdT-3′(SEQ ID NO:2).

Gel shift assays and determination of dissociation constant: The RNAaptamers were treated by calf intestine phosphatase (CIP) to remove theinitiating 5′-triphosphate and were subsequently labeled at the 5′termini with T4 polynucleotide kinase and γ-³²P-ATP. The gp120 proteinwas serially diluted to the desired concentrations (0-640 nM). Aconstant amount of end-labeled RNA (10 nM) was incubated withcorresponding concentrations gp120 protein in binding buffer (10 mMHEPES pH 7.4, 150 mM NaCl, 1 mM CaCl₂, 1 mM MgCl₂, 2.7 mM KCl, 10 mMDTT, 0.01% BSA and tRNA) at room temperature. After 30 min ofincubation, 20 μL of binding reaction was loaded onto a 5%non-denaturing polyacrylamide gel. The gel was exposed to a Phosphorimaging screen and quantified using a Typhoon scanner. The dissociationconstants were calculated using non-linear curve regression with a GraphPad Prism.

Cell culture: HEK 293 cells and CEM cells were purchased from ATCC andcultured in DMEM and RPMI 1640 supplemented with 10% FBS respectively,according to their respective data sheets. CHO-WT and CHO-EE cells wereobtained through the AIDS Research and Reference Reagent Program,Division of AIDS, NIAID, NIH. They are grown in GMEM-S. Cells werecultured in a humidified 5% CO₂ incubator at 37° C. PBMC. Blood sampleswere obtained from healthy donors from the City of hope National MedicalCenter (clinic personnel). PBMC were isolated from whole blood bycentrifugation through Ficoll-Hypaque solution (Histopaque-1077, Sigma).CD8 cells (T-cytotoxic/suppressor cells) were depleted from PBMC byusing Dynabeads CD8 (Invitrogen, CA) according to the manufacturer'sinstructions. CD8⁺ T cell-depleted PBMC were washed twice in PBS andresuspended in culture medium (RPMI 1640 with 10% FBS, 1×PenStrep and100 U/mL interleukin-2). Cells were cultured in a humidified 5% CO₂incubator at 37° C.

Cell-surface binding of aptamer-siRNA chimeras (flow cytometryanalysis): CHO-WT gp160 or CHO-EE cells were washed with PBS,trypsinized and detached from the plates. After washing cells twice with500 μL binding buffer. Cell pellets were resuspended in binding bufferand incubated at 37° C. for 30 mM. Cells were then pelleted andresuspended in 50 μL of prewarmed binding buffer containing either 400nM Cy3-labeled aptamer or Chimera RNAs. After incubation at 37° C. for40 min, cells were washed three times with 500 μL of prewarmed bindingbuffer, and finally resuspended in 350 μL of binding buffer prewarmed to37° C. and analyzed by flow cytometry.

Cellular binding and uptake studies (confocal microscopy analysis): TheCHO-gp160 and CHO-EE cells lines were grown in an 8-well chambered-slidewith seeding at 0.5×10⁵ in GMEM-S medium to allow about 70% confluencein 24 h. On the day of the experiments, cells were washed with 250 μL ofprewarmed PBS and incubated with 250 μL of prewarmed complete growthmedium for 30 min at 37° C. Cy3-labeled RNAs at 40 nM finalconcentration were added into the media and incubated at 37° C. for 2hrs. Subsequently, cells were washed three times with 250 μL ofprewarmed PBS, fixed with 4% formaldehydes for 15 min. The cells werestained by treatment with 100 μL of Vybrant Cell-Labeling Solution (DIOmembrane dye, Molecular Probes, Invitrogen) according to themanufacturer's instructions. The images were collected using a Zeiss LSM510 upright 2 photon confocal microscopy system under water immersion at40 magnifications.

HIV-1 challenges and p24 antigen assay: CEM cells or PBMCs were infectedwith HIV IIIB or NL4-3 for 5 days. Prior to aptamer treatments theinfected cells were gently washed with PBS three times to remove freevirus. 2×10⁴ infected cells and 3×10⁴ uninfected cells were incubatedwith refolded RNAs at 400 nM final concentration in 96-well plates at37° C. The culture supernatants were collected at different times (3 d,5 d, 7 d, 9 d and 11 d). The p24 antigen analyses were performed using aCoulter HIV-1 p24 Antigen Assay (Beckman Coulter) according to themanufacturer's instructions.

qRT-PCR analysis: CEM cells were infected with HIV IIIB or NL4-3 for 5days. Prior to analyses, the infected-CEM cells were gently washed 3times to eliminate free virus. The infected CEM cells were treateddirectly with the aptamer or Ch L-1 (400 nM). After 7 days, total RNAswere isolated with STAT-60 (TEL-TEST “B”, Friendswood, Tex.). Expressionof the tat/rev coding RNAs was analyzed by quantitative RT-PCR using 2×iQ SyberGreen Mastermix (BIO-RAD) and specific primer sets at a finalconcentration of 400 nM. Primers were as follows: tat/rev forwardprimer: 5′-GGCGTTACTCGACAGAGGAG-3′ (SEQ ID NO:22); tat/rev reverseprimer: 5′-TGCTTTGATAGAGAAGCTTGATG-3′ (SEQ ID NO:23); GAPDH forwardprimer 1: 5′-CATTGACCTCAACTACATG-3′ (SEQ ID NO:24); GAPDH reverse primer2: 5′-TCTCCATGGTGGTGAAGAC-3′ (SEQ ID NO:25). RNA-Stat60 was used toextract total RNA according to the manufacturer's instruction(Tel-Test). Residual DNA was digested using the DNA-free kit per themanufacturer's instructions (Ambion). cDNA was produced using 2 μg oftotal RNA Moloney murine leukemia virus reverse transcriptase and randomprimers in a 15 μL, reaction according to the manufacturer'sinstructions (Invitrogen). GAPDH expression was used for normalizationof the qPCR data.

Example 10 2′-F-Substituted Aptamers

We described above a novel dual inhibitory function anti-gp120aptamer-siRNA chimera delivery system for HIV-1 therapy. In order toincrease the applicability and efficacy of aptamers in clinical therapy,in the present of study, new 2′-F substituted RNA aptamers that bind tothe HIV-1_(Ba-L) gp120 protein were isolated from an RNA library byusing a process called SELEX (Systematic Evolution of Ligands byEXponential enrichment) (41, 42, 44, 45). Scintillation measurement andgel shift assays showed that the selected RNA aptamers (FIG. 11A)specifically bind to the target protein with low to mid nanomolardissociation constants (FIG. 11B). Flow cytometry data (FIG. 12A) andconfocal microscopy (FIG. 12B) indicated that the aptamers are able tospecifically bind and be internalized by cells expressing HIV gp160. Inaddition, these aptamers also have been shown to potently neutralize abroad range of HIV-1 strains (FIG. 13). Further, we have developedaptamer-siRNA chimeric RNAs (FIGS. 14A and 14B) to specifically deliverfunctional siRNAs into HIV-1 infected cells. These chimeras RNA alsospecifically inhibit HIV-1 infectivity in human leukemic CEM cells(FIGS. 15A and 15B) and Peripheral Blood Mononuclear cells (PBMC)culture (FIGS. 15C and 15D).

These results demonstrate that the aptamers are not only expected toprovide an inhibitor to fight HIV-1, but also act as delivery moleculesfor siRNAs and perhaps other small RNA inhibitors.

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What is claimed is:
 1. A composition comprising a molecule and aphysiologically acceptable carrier, wherein the molecule comprises anaptamer linked to a Dicer substrate siRNA, wherein the aptamer is ananti-gp120 aptamer, wherein the Dicer substrate siRNA is directedagainst an HIV-1 target sequence, wherein the HIV-1 target sequence istat/rev, and wherein the aptamer is selected from: (a) an anti-gp120aptamer that comprises the nucleotide sequence set forth in SEQ ID NO:8, (b) an anti-gp120 aptamer that comprises the nucleotide sequence setforth in SEQ ID NO: 9, and (c) an anti-gp120 aptamer of (a) or (b) whichis modified to contain 2′-F substituted nucleotides.
 2. The compositionof claim 1, wherein the aptamer is between 10 and 300 nucleotides inlength.
 3. The composition of claim 2, wherein the aptamer is between 30and 100 nucleotides in length.
 4. The composition of claim 1, whereinthe Dicer substrate siRNA contains 2′-F substituted nucleotides.
 5. Acomposition comprising a molecule and a physiologically acceptablecarrier, wherein the molecule comprises an aptamer linked to a Dicersubstrate siRNA, wherein the aptamer is an anti-gp120 aptamer, whereinthe Dicer substrate siRNA is a double stranded nucleic acid comprising asense strand and an antisense strand, wherein the Dicer substrate siRNAis directed against an HIV-1 target sequence, wherein the HIV-1 targetsequence is tat/rev, and wherein the aptamer is selected from: (a) ananti-gp120 aptamer that comprises the nucleotide sequence set forth inSEQ ID NO: 8, (b) an anti-gp120 aptamer that comprises the nucleotidesequence set forth in SEQ ID NO: 9, and (c) an anti-gp120 aptamer of (a)or (b) which is modified to contain 2′-F substituted nucleotides.
 6. Thecomposition of claim 5, wherein the aptamer is between 10 and 300nucleotides in length.
 7. The composition of claim 6, wherein theaptamer is between 30 and 100 nucleotides in length.
 8. The compositionof claim 5, wherein the sense strand has a 5′ end and a 3′ end, andwherein the 3′ end has an overhang comprising 1 to 3 nucleotides.
 9. Thecomposition of claim 5, wherein the antisense strand has a 5′ end and a3′ end, and wherein the 3′ end contains a modifier.
 10. The compositionof claim 9, wherein the modifier is one or more nucleotides selectedfrom the group consisting of deoxyribonucleotides,dideoxyribonucleotides, and acyclonucleotides.
 11. The composition ofclaim 9, wherein the modifier is a fluorescent molecule.
 12. Thecomposition of claim 5, wherein the antisense strand has a 5′ end and a3′ end, and wherein the antisense strand has a 5′ phosphate group. 13.The composition of claim 5, wherein the sense strand is selected fromthe group consisting of: (a) a sense strand that comprises thenucleotide sequence set forth in SEQ ID NO: 10; and (b) a sense strandthat comprises the nucleotide sequence set forth in SEQ ID NO:
 11. 14.The composition of claim 5, wherein the antisense strand is selectedfrom the group consisting of: (a) an antisense strand that comprises thenucleotide sequence set forth in SEQ ID NO: 2; (b) an antisense strandthat comprises the nucleotide sequence set forth in SEQ ID NO: 3; and(c) an antisense strand that comprises the nucleotide sequence set forthin SEQ ID NO:
 18. 15. The composition of claim 5, wherein the anti-gp120aptamer is linked to the siRNA sense strand and forms an anti-gp120aptamer-siRNA sense strand chimera, and wherein the anti-gp120aptamer-siRNA sense strand chimera is selected from the group consistingof: (a) an anti-gp120 aptamer-siRNA sense strand chimera that comprisesthe nucleotide sequence set forth in SEQ ID NO: 1; (b) an anti-gp120aptamer-siRNA sense strand chimera that comprises the nucleotidesequence set forth in SEQ ID NO: 13; (c) an anti-gp120 aptamer-siRNAsense strand chimera that comprises the nucleotide sequence set forth inSEQ ID NO: 14; (d) an anti-gp120 aptamer-siRNA sense strand chimera thatcomprises the nucleotide sequence set forth in SEQ ID NO: 15; (e) ananti-gp120 aptamer-siRNA sense strand chimera that comprises thenucleotide sequence set forth in SEQ ID NO: 16; (f) an anti-gp120aptamer-siRNA sense strand chimera that comprises the nucleotidesequence set forth in SEQ ID NO: 17; (g) an anti-gp120 aptamer-siRNAsense strand chimera that comprises the nucleotide sequence set forth inSEQ ID NO: 32; and (h) an anti-gp120 aptamer-siRNA sense strand chimerathat comprises the nucleotide sequence set forth in SEQ ID NO:
 33. 16.The composition of claim 5, wherein the aptamer contains 2′-Fsubstituted nucleotides.
 17. The composition of claim 5, wherein theDicer substrate siRNA contains 2′-F substituted nucleotides.
 18. Amethod of treating HIV1 in a patient in need thereof, the methodcomprising administering the composition of claim 1 to the patient. 19.A method of treating HIV1 in a patient in need thereof, the methodcomprising administering the composition of claim 5 to the patient.